Contacts of the helix formed by residues 380 - 390 (chain B) in PDB entry 3OPY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B CYS* 1.3 72.5 - - - +
381B TRP* 1.3 58.7 + - - +
382B LEU 3.4 2.2 - - - -
383B GLY 3.3 3.3 + - - -
384B LEU* 2.8 33.3 + - - +
397B ILE* 3.7 24.6 - - - +
398B PRO* 4.2 1.3 - - - -
399B GLU* 3.1 27.1 + - - -
431B ALA* 5.3 1.8 - - - -
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Residues in contact with TRP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ASP 3.9 5.6 - - - +
334B ASN* 3.2 36.2 - - + +
340B ASP 4.7 2.6 + - - -
345B ALA* 3.5 36.3 - - + -
346B PHE* 3.7 34.1 - + - -
349B LEU* 4.1 13.7 - - + -
379B CYS* 3.5 22.2 - - - -
380B GLY* 1.3 75.6 - - - +
382B LEU* 1.3 84.7 + - + +
384B LEU* 3.3 8.2 + - + -
385B LEU* 2.8 72.0 + - + +
399B GLU* 5.3 0.2 - - - -
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 3.3 28.7 - - + +
333B ASP* 4.4 9.1 + - - +
345B ALA 3.6 12.3 - - - +
348B SER* 3.9 5.6 - - - +
349B LEU* 3.5 36.6 - - - +
352B ILE* 3.9 10.7 - - + +
374B VAL* 4.1 7.9 - - + -
375B MET 3.3 24.0 - - - +
376B GLY* 4.6 3.6 - - - -
379B CYS 5.4 1.0 + - - +
380B GLY 3.4 0.6 - - - -
381B TRP* 1.3 90.1 - - + +
383B GLY* 1.3 57.2 + - - +
385B LEU 3.9 0.2 - - - -
386B ALA* 2.9 34.2 + - - +
468B GLN* 3.7 10.5 - - - +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 4.5 7.1 - - - +
380B GLY* 3.3 8.3 + - - -
382B LEU* 1.3 77.6 - - - +
384B LEU* 1.3 55.3 + - - +
386B ALA* 3.8 1.3 - - - +
387B GLY* 2.9 28.2 + - - -
395B ILE* 3.9 9.4 - - - +
397B ILE* 3.9 16.6 - - - -
429B ILE* 4.0 20.9 - - - +
431B ALA* 5.5 2.2 - - - -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B GLY 2.8 20.3 + - - +
381B TRP* 3.8 7.2 - - + +
383B GLY* 1.3 71.6 - - - +
385B LEU* 1.4 71.6 + - + +
387B GLY* 3.4 1.7 + - - -
388B LEU* 2.9 40.1 + - + +
395B ILE* 3.8 24.8 - - + +
397B ILE* 4.3 10.1 - - + -
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B PHE* 4.5 9.2 - - + -
349B LEU* 3.7 26.5 - - + -
381B TRP* 2.8 71.8 + - + +
384B LEU* 1.4 85.1 - - + +
386B ALA* 1.4 53.8 + - - +
388B LEU* 3.2 14.6 + - + +
389B ALA* 2.8 36.2 + - - +
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B LEU* 3.5 12.4 - - + +
352B ILE* 3.7 29.6 - - + -
353B CYS* 3.9 8.5 - - - -
356B ILE* 4.2 2.9 - - + -
374B VAL* 5.5 0.2 - - + -
382B LEU 2.9 19.3 + - - +
383B GLY* 3.8 4.3 - - - +
385B LEU* 1.4 72.8 - - - +
387B GLY* 1.3 53.8 + - - +
389B ALA 3.3 0.2 + - - -
390B THR* 2.6 44.9 + - - +
429B ILE* 4.0 10.8 - - + -
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Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLY 2.9 18.4 + - - -
384B LEU 3.7 2.0 - - - -
386B ALA* 1.3 76.2 - - - +
388B LEU* 1.3 54.5 + - - +
391B SER* 3.0 10.6 + - - -
392B ALA* 2.9 34.7 + - - +
395B ILE* 4.0 8.1 - - - -
429B ILE* 3.5 14.9 - - - +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B LEU* 2.9 26.5 + - + +
385B LEU* 3.2 16.1 + - + +
387B GLY* 1.3 74.8 - - - +
389B ALA* 1.4 60.9 + - - +
391B SER* 3.3 17.4 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B LEU* 5.4 3.4 - - + -
353B CYS* 3.8 24.0 - - + -
357B ASP* 5.6 0.5 - - - +
385B LEU 2.8 19.8 + - - +
386B ALA 3.8 0.2 - - - +
388B LEU* 1.4 72.8 - - - +
390B THR* 1.3 59.9 + - + +
391B SER* 4.0 0.7 + - - -
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B CYS* 3.9 24.5 - - + -
356B ILE* 3.6 44.2 - - + +
357B ASP* 4.2 12.6 - - - +
360B ASP* 4.5 12.7 - - - +
386B ALA 2.6 29.5 + - - +
387B GLY* 4.1 2.1 + - - -
389B ALA* 1.3 76.0 - - - +
391B SER* 1.4 69.8 + - - +
392B ALA* 3.3 5.9 + - - +
427B ILE* 5.7 2.1 - - - +
429B ILE* 4.3 1.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il